3.4 Building on Platforms with Parallel I/O
NetCDF makes available the parallel I/O features of HDF5 and the
parallel-netcdf libraries, allowing parallel I/O from netCDF-4 linked
programs.
3.4.1 Building HDF5 for Parallel I/O
For parallel I/O to work, HDF5 must be installed with
–enable-parallel, and an MPI library (and related libraries) must be
made available to the HDF5 configure. This can be accomplished with
the mpicc wrapper script, in the case of MPICH2.
The following works to build HDF5 with parallel I/O on our netCDF
testing system:
CC=mpicc ./configure --enable-parallel --prefix=/shecky/local_par --with-zlib=/shecky/local_par --disable-shared && make check install
3.4.2 The parallel-netcdf Library
Optionally, the parallel-netcdf library should also be installed, and
you should configure with --enable-pnetcdf. (Note: the previously
recommended Unidata replacement pnetcdf.h should no longer be used!).
3.4.3 Building NetCDF
To build netCDF with parallel I/O, build as usual, but point the
configure at a version of HDF5 that has been built for parallel I/O.
CPPFLAGS=-I/shecky/local_par/include
CXXFLAGS=-I/shecky/local_par/include
FFFLAGS=-I/shecky/local_par/include
FCFLAGS=-I/shecky/local_par/include LDFLAGS=-L/shecky/local_par/lib
FC=mpif90 CXX=mpicxx CC=mpicc ./configure
make check install
To enable the parallel tests, specify –enable-parallel-tests as an
option to configure. These tests will be run as mpiexec calls. This
may not be appropriate on all systems, especially those which use some
queue for jobs.
To use parallel-netcdf to perform parallel I/O on classic and 64-bit
offset files, use the –enable-pnetcdf option.
For parallel builds the netCDF examples are not built. This is to
avoid cluttering them with MPI_Init/Finalize calls.
